Efficient HF exchange evaluation through Fourier convolution in Cartesian grid for orbital-dependent density functionals.

We present a purely numerical approach in a Cartesian grid, for efficient computation of the Hartree-Fock (HF) exchange contribution in the HF and density functional theory models. This takes inspiration from a recently developed algorithm by Liu et al., in 2017, where the rate-determining step is the accurate evaluation of electrostatic potential. This introduces the Fourier convolution theorem in conjunction with a range-separated Coulomb interaction kernel. The latter is efficiently mapped into a real grid through a simple optimization procedure, giving rise to a constraint in the range-separated parameter. The overall process offers logarithmic scaling with respect to the molecular size. It is then extended toward global hybrid functionals such as B3LYP, PBE0, and BHLYP within pseudopotential Kohn-Sham theory, through an LCAO-MO ansatz in a Cartesian grid, developed earlier in our laboratory. For the sake of comparison, a parallel semi-numerical approach has also been worked out that exploits the familiar Obara-Saika recursion algorithm without any additional techniques. An excellent agreement between these two routes is demonstrated through total energy and orbital energy in a series of atoms and molecules (including 10 π-electron molecules), employing an LANL2DZ-type basis function. A critical analysis of these two algorithms reveals that the proposed numerical scheme could lead to very attractive and competitive scaling. The success of our approach also enables us for further development of optimally tuned range-separated hybrid and hyper functionals.

Mechanism of N-Acylthiourea-mediated activation of human histone deacetylase 8 (HDAC8) at molecular and cellular levels.

We reported previously that an N-acylthiourea derivative (TM-2-51) serves as a potent and isozyme-selective activator for human histone deacetylase 8 (HDAC8). To probe the molecular mechanism of the enzyme activation, we performed a detailed account of the steady-state kinetics, thermodynamics, molecular modeling, and cell biology studies. The steady-state kinetic data revealed that TM-2-51 binds to HDAC8 at two sites in a positive cooperative manner. Isothermal titration calorimetric and molecular modeling data conformed to the two-site binding model of the enzyme-activator complex. We evaluated the efficacy of TM-2-51 on SH-SY5Y and BE(2)-C neuroblastoma cells, wherein the HDAC8 expression has been correlated with cellular malignancy. Whereas TM-2-51 selectively induced cell growth inhibition and apoptosis in SH-SY5Y cells, it showed no such effects in BE(2)-C cells, and this discriminatory feature appears to be encoded in the p53 genotype of the above cells. Our mechanistic and cellular studies on HDAC8 activation have the potential to provide insight into the development of novel anticancer drugs.

Thermodynamics of binding of structurally similar ligands to histone deacetylase 8 sheds light on challenges in the rational design of potent and isozyme-selective inhibitors of the enzyme.

Among the different histone deacetylase (HDAC) isozymes, HDAC8 is the most highly malleable enzyme, and it exhibits the potential to accommodate structurally diverse ligands (albeit with moderate binding affinities) in its active site pocket. To probe the molecular basis of this feature, we performed detailed thermodynamic studies of the binding of structurally similar ligands, which differed with respect to the "cap", "linker", and "metal-binding" regions of the suberoylanilide hydroxamic acid (SAHA) pharmacophore, to HDAC8. The experimental data revealed that although the enthalpic (ΔH°) and entropic (ΔS°) changes for the binding of individual SAHA analogues to HDAC8 were substantially different, their binding free energies (ΔG°) were markedly similar, conforming to a strong enthalpy-entropy compensation effect. This effect was further observed in the temperature-dependent thermodynamics of binding of all SAHA analogues to the enzyme. Notably, in contrast to other metalloenzymes, our isothermal titration calorimetry experiments (performed in different buffers of varying ionization enthalpies) suggest that depending on the ligand, its zinc-binding group may or may not be deprotonated upon the binding to HDAC8. Furthermore, the heat capacity changes (ΔCp°) associated with the ligand binding to HDAC8 markedly differed from one SAHA analogue to the other, and such features could primarily be rationalized in light of the dynamic flexibility in the enzyme structure in conjunction with the reorganization of the active site resident water molecules. Arguments are presented that although the binding thermodynamic features described above would facilitate identification of weak to moderately tight-binding HDAC8 inhibitors (by a high-throughput and/or virtual screening of libraries of small molecules), they would pose major challenges for the structure-based rational design of highly potent and isozyme-selective inhibitors of human HDAC8.

Kinetic and thermodynamic rationale for suberoylanilide hydroxamic acid being a preferential human histone deacetylase 8 inhibitor as compared to the structurally similar ligand, trichostatin a.

Of the different hydroxamate-based histone deacetylase (HDAC) inhibitors, suberoylanilide hydroxamic acid (SAHA) has been approved by the Food and Drug Administration for the treatment of T-cell lymphoma. Interestingly, a structurally similar inhibitor, trichostatin A (TSA), which has a higher in vitro inhibitory potency against HDAC8, reportedly shows poor efficacy in clinical settings. To gain molecular insight into this discriminatory feature, we performed transient kinetic and isothermal titration calorimetric studies for the interaction of SAHA and TSA with the recombinant form of human HDAC8. The transient kinetic data revealed that the binding of both inhibitors to the enzyme showed biphasic profiles, which represented an initial encounter of the enzyme with the inhibitor followed by the isomerization of the transient enzyme-inhibitor complexes. The temperature-dependent transient kinetic studies with these inhibitors revealed that the bimolecular process is primarily dominated by favorable enthalpic changes, as opposed to the isomerization step, which is solely contributed by entropic changes. The standard binding enthalpy (ΔH°) of SAHA, deduced from the transient kinetic as well as the isothermal titration calorimetric experiments, was 2-3 kcal/mol higher than that of TSA. The experimental data presented herein suggest that SAHA serves as a preferential (target-specific and -selective) HDAC8 inhibitor as compared to TSA. Arguments that the detailed kinetic and thermodynamic studies may guide the rational design of HDAC inhibitors as therapeutic agents are presented.

Organocatalytic, highly enantioselective vinylogous Mukaiyama-Michael reaction of acyclic dienol silyl ethers.

Now also acyclic: The first catalytic, enantioselective, vinylogous Michael reaction of linear, acyclic dienol silyl ethers was achieved. The reaction, based upon the principle of iminium ion catalysis, delivered 1,7-dioxo compounds in one step with good yields, complete regio-, and excellent enantioselectivity. γ-Substituted dienol silyl ethers furnished products with two new stereogenic centers with good diastereoselectivity. Ms = mesityl, PNBA = para-nitrobenzoic acid.

RMAC study: A randomized study for evaluation of metronomic adjuvant chemotherapy in recurrent head and neck cancers post salvage surgical resection in those who are ineligible for re-irradiation.

BACKGROUND: Adjuvant re-chemoradiation after salvage surgery improves disease-free survival in recurrent head and neck cancer. However, most patients are ineligible for re-irradiation and are kept on observation. We investigated the efficacy of metronomic adjuvant chemotherapy (MAC) in this group of patients compared to observation. METHODS: This was a randomized integrated phase II/III clinical trial. Adults with recurrent head and neck cancer, who had undergone salvage surgery, but were ineligible for adjuvant re-irradiation were randomized in a 1:1 ratio to either MAC arm or observation. MAC consisted of weekly oral methotrexate (at a dose of 15 mg per square meter of body surface area) and celecoxib (at a dose of 200 mg orally twice daily) for 6 months. The primary endpoint of phase 2 was disease-free survival (DFS) while that of phase 3 was overall survival (OS). For phase 2, to detect an improvement in the hazard ratio (HR) 0.67 with MAC, with a type 1 error of 10% (1-sided), type 2 error of 30%, 105 patients were required. While for phase 3, with a target HR of 0.77, with a type 1 error of 5%, type 2 error of 20%, 318 patients were required. Here we report the results of phase 2 part of the study. RESULTS: At a median follow up of 30.2 months (95% confidence interval (CI), 25.3 to 35.1) the 1 year and 2-year DFS were 57.4% (95% CI, 42.8-69.5) and 37.6% (95% CI, 24.1-51) in MAC arm whereas the corresponding numbers were 62.3% (95% CI, 47.8 to 73.8) and 54.2%(95% CI, 39.8 to 66.5) in observation arm, respectively (hazard ratio for progression, 1.45; 95% CI, 0.87 to 2.47; P = 0.15). In the MAC arm, the 1 and 2 year OS was 78.7% (95% CI, 64.9 to 87.6) and 48% (95% CI, 34.1 to 62).The corresponding figures in the observation arm were 79.2% (95% CI, 65.7 to 87.9) and 65.5% (95% CI, 50.9 to 76.7) (hazard ratio for death, 1.7, 95% CI, 0.94 to 3.08; P = 0.08). CONCLUSION: The adjuvant 6-month metronomic schedule was ineffective in improving outcomes in recurrent head and neck cancers post salvage surgery who are ineligible for re-radiation. TRIAL REGISTRATION: Clinical trial registry of India (CTRI)- CTRI/2016/04/006872 [Registered on 26/4/2016].

Coumarin-suberoylanilide hydroxamic acid as a fluorescent probe for determining binding affinities and off-rates of histone deacetylase inhibitors.

Histone deacetylases (HDACs) are intimately involved in epigenetic regulation and, thus, are one of the key therapeutic targets for cancer, and two HDAC inhibitors, namely suberoylanilide hydroxamic acid (SAHA) and romidepsin, have been recently approved for cancer treatment. Because the screening and detailed characterization of HDAC inhibitors has been time-consuming, we synthesized coumarin-SAHA (c-SAHA) as a fluorescent probe for determining the binding affinities (K(d)) and the dissociation off-rates (k(off)) of the enzyme-inhibitor complexes. The determination of the above parameters relies on the changes in the fluorescence emission intensity (λ(ex)=325 nm, λ(em)=400 nm) of c-SAHA due to its competitive binding against other HDAC inhibitors, and such determination neither requires employment of polarization accessories nor is dependent on the fluorescence energy transfer from the enzyme's tryptophan residues to the probe. Our highly sensitive and robust analytical protocol presented here is applicable to most of the HDAC isozymes, and it can be easily adopted in a high-throughput mode for screening the HDAC inhibitors as well as for quantitatively determining their K(d) and k(off) values.

Histone deacetylase activators: N-acetylthioureas serve as highly potent and isozyme selective activators for human histone deacetylase-8 on a fluorescent substrate.

We report, for the first time, that certain N-acetylthiourea derivatives serve as highly potent and isozyme selective activators for the recombinant form of human histone deacetylase-8 in the assay system containing Fluor-de-Lys as a fluorescent substrate. The experimental data reveals that such activating feature is manifested via decrease in the K(m) value of the enzyme's substrate and increase in the catalytic turnover rate of the enzyme.

Bis(propan-2-yl) [(2S,3S)-2-hydr-oxy-3-nitro-butan-2-yl]phospho-nate.

In the title compound, C(10)H(22)NO(6)P, a staggered conformation is found when the mol-ecule is viewed down the central P-C bond, with the oxo and hydr-oxy groups gauche to each other. The crystal structure features supra-molecular chains of helical topology propagating along the b axis, mediated by O-H⋯O hydrogen bonds.

Bis(propan-2-yl) [(1S)-1-(4-fluoro-phen-yl)-1-hydr-oxy-2-nitro-ethyl]phospho-nate.

In the title compound, C(14)H(21)FNO(6)P, a staggered conformation about the central P-C bond occurs, with the oxo and hydroxyl groups occupying diagonally opposite positions. The crystal structure features supra-molecular chains mediated by O-H⋯O hydrogen bonds, which propagate in the a-axis direction. A C-H⋯O inter-action consolidates the chains. Disorder was resolved for one of the isopropyl groups with a 0.60 (2):0.40 (2) occupancy ratio for the two components.

Synthesis of 2,3,4-Trisubstituted Thiochromanes using an Organocatalytic Enantioselective Tandem Michael-Henry Reaction.

Enantioenriched 2,3,4-trisubstituted thiochromanes have been synthesized by using a cupreine-catalyzed tandem Michael addition-Henry reaction between 2-mercaptobenzaldehydes and ß-nitrostyrenes. Good diastereoselectivities and enantioselectivities were obtained for the title compounds, which may be further improved through a single recrystallization (up to 98% de and> 99% ee).

Organocatalytic Highly Enantioselective Tandem Michael-Knoevenagel Reaction for the Synthesis of Substituted Thiochromanes.

Enantioenriched tetrasubstituted thiochromanes have been synthesized using a tandem Michael addition-Knoevenagel reaction between 2-mercaptobenzaldehydes and benzylidenemalonates with a 9-epi-aminoquinine thiourea derivative as the catalyst. Steric and electron effects were found to affect profoundly the enantioselectivity and diastereoselectivity of the reaction.

Organocatalytic highly enantioselective nitroaldol reaction of alpha-ketophosphonates and nitromethane.

[reaction: see text] The first organocatalytic highly enantioselective nitroaldol reaction of alpha-ketophosphonates and nitromethane has been realized by using cupreine (2) or 9-O-benzylcupreine (3) as the catalyst. Both catalysts are highly reactive and highly enantioselective. alpha-Hydroxy-beta-nitrophosphonates have been synthesized in good yields and excellent enantioselectivities (>or=90% ee) at a low catalyst loading (5 mol %). These nitroaldol products may be reduced to the biologically significant beta-amino-alpha-hydroxyphosphonates with complete retention of the stereochemistry.

Inverse-electron-demand hetero-Diels-Alder reaction of beta,gamma-unsaturated alpha-ketophosphonates catalyzed by prolinal dithioacetals.

Some novel prolinal dithioacetal derivatives were studied as catalysts for the inverse-electron-demand hetero-Diels-Alder reaction of enolizable aldehydes and beta,gamma-unsaturated alpha-ketophosphonates. The corresponding 5,6-dihydro-4H-pyran-2-ylphosphonates were obtained in good ee values (up to 94% ee).

Synthesis of Prolinal Dithioacetals as Catalysts for the Highly Stereoselective Michael Addition of Ketones and Aldehydes to beta-Nitrostyrenes.

Catalytic highly enantioselective (up to >99% ee) and diastereoselective (up to 99% de) direct Michael addition of ketones and aldehydes to beta-nitrostyrenes have been achieved with readily accessible and highly tunable prolinal dithioacetal catalysts.

Highly diastereoselective palladium-catalyzed indium-mediated allylation of chiral hydrazones.

The general and efficient palladium-catalyzed indium-mediated allylation of chiral hydrazones was accomplished with excellent yield (72-92%) and diastereoselectivity (up to 99:1). The development of this reaction and the substrate scope are described. The conversion was found to be proportional to the phosphine concentration, which provided insight into the mechanism and competing pathways of the redox transmetalation process.

Indium(I) iodide-mediated cleavage of diphenyl diselenide. An efficient one-pot procedure for the synthesis of unsymmetrical diorganyl selenides.

A simple and efficient procedure has been developed for the synthesis of unsymmetrical diorganyl selenides through a one-pot indium(I) iodide-mediated reaction of alkyl halide and diphenyl diselenide in methylene chloride at room temperature. [reaction: see text]

Indium(I) iodide-promoted cleavage of diaryl diselenides and disulfides and subsequent condensation with alkyl or acyl halides. One-pot efficient synthesis of diorganyl selenides, sulfides, selenoesters, and thioesters.

Diphenyl diselenides and disulfides undergo facile cleavages by indium(I) iodide and the corresponding generated selenate and thiolate anions condense in situ with alkyl or acyl halides present in the reaction mixture. Thus, a simple, efficient, and general procedure has been developed for the synthesis of unsymmetrical diorganyl selenides, sulfides (thioethers), selenoesters, and thioesters by this one-pot reaction at room temperature.